Our Approach

Our group is an integrated computational and experimental lab that uses and develops computational tools and statistical methods to both analyze experimental data as well as inform our experiments. Our lab also utilizes and develops key experimental protocols needed to answer our key questions and test specific hypothesis that arise from our data. We do not make a clear distinction between "computational projects" and "experimental projects", our projects are goal centered and we use all of the tools available to us to achieve this goal.

Biochemistry

Our group utilizes biochemistry to purify RNA-Protein complexes and map their sites of interactions. We utilize methods for RNA-Protein complex purification and identification using quantitative mass-spectrometry. We utilize and adapt various crosslinking methods to define lincRNA complexes in vivo.

Computational Biology

Our group develops novel computational tools and methods to understand and integrate large-scale datasets to test specific biological hypotheses and learn key principles. Some of our tools and software can be downloaded here.

Functional and Cell Biology

Our group utilizes methods to perturb lincRNA genes to define the function of lincRNA genes and specific domains. We focus on mouse embryonic stem cells to define the function of lincRNAs in cell biology and determining how lincRNAs control gene expression and cell state decision. Protocols and tools can be downloaded here.

Genomics

Our group utilizes "hypothesis-driven genomics" to determine the function and mechanism of lincRNAs in an unbiased manner. We use genomic approaches to read out various experimental assays including gene expression levels, RNA-protein interactions, and RNA localization patterns. We develop and adapt new experimental strategies to increase efficiency and reduce costs of key genomic assays. Protocols, software, and data can be downloaded here.

Molecular Biology

Our group utilizes and develops molecular biology protocols to define RNA complexes, interaction sites, and function. We adapt existing protocols and develop new protocols to address key questions. Protocols and tools can be downloaded here.